Argonaute CLIP Defines a Deregulated miR-122-Bound Transcriptome that Correlates with Patient Survival in Human Liver Cancer

• Published in: Molecular cell 2017-08, Vol.67 (3), p.400-410.e7
• Main Authors: Luna, Joseph M., Barajas, Juan M., Teng, Kun-yu, Sun, Hui-Lung, Moore, Michael J., Rice, Charles M., Darnell, Robert B., Ghoshal, Kalpana
• Format: Article
• Language: English
• Subjects: 3' Untranslated Regions; Animals; Argonaute; Argonaute Proteins - genetics; Argonaute Proteins - metabolism; BCL9; Binding Sites; Carcinoma, Hepatocellular - genetics; Carcinoma, Hepatocellular - metabolism; Carcinoma, Hepatocellular - mortality; Carcinoma, Hepatocellular - pathology; Case-Control Studies; Cell Line, Tumor; Cell Proliferation; CLIP; Computational Biology; Databases, Genetic; Down-Regulation; Exons; Gene Expression Regulation, Neoplastic; gene regulation; Genome-Wide Association Study; Genotype; HCC; hepatocellular carcinoma; Humans; Immunoprecipitation - methods; Intracellular Signaling Peptides and Proteins - genetics; Intracellular Signaling Peptides and Proteins - metabolism; Liver Neoplasms - genetics; Liver Neoplasms - metabolism; Liver Neoplasms - mortality; Liver Neoplasms - pathology; Mice; Mice, Knockout; MicroRNAs - genetics; MicroRNAs - metabolism; miR-122; Neoplasm Proteins - genetics; Neoplasm Proteins - metabolism; Phenotype; RNA Interference; Species Specificity; Time Factors; Transcription Factors; Transcription, Genetic; Transcriptome; Transfection; Wnt; Wnt Signaling Pathway
• ISSN: 1097-2765; 1097-4164
• DOI: 10.1016/j.molcel.2017.06.025

MicroRNA-122, an abundant and conserved liver-specific miRNA, regulates hepatic metabolism and functions as a tumor suppressor, yet systematic and direct biochemical elucidation of the miR-122 target network remains incomplete. To this end, we performed Argonaute crosslinking immunoprecipitation (Argonaute [Ago]-CLIP) sequencing in miR-122 knockout and control mouse livers, as well as in matched human hepatocellular carcinoma (HCC) and benign liver tissue to identify miRNA target sites transcriptome-wide in two species. We observed a majority of miR-122 binding on 3′ UTRs and coding exons followed by extensive binding to other genic and non-genic sites. Motif analysis of miR-122-dependent binding revealed a G-bulged motif in addition to canonical motifs. A large number of miR-122 targets were found to be species specific. Upregulation of several common mouse and human targets, most notably BCL9, predicted survival in HCC patients. These results broadly define the molecular consequences of miR-122 downregulation in hepatocellular carcinoma. [Display omitted] •Genome-wide miRNA binding sites were elucidated in miR-122 KO mice and human HCC•Widespread, non-canonical, and species-specific miR-122 binding was observed•miR-122 binding sites in human HCC revealed a core set of conserved targets•Conserved miR-122 targets, most notably BCL9, correlated with human HCC survival Lack of the liver-specific microRNA-122 spontaneously results in hepatocellular carcinoma in mice. Luna et al. provide a comprehensive and biochemically defined catalog of miR-122 targets in mice and humans to uncover novel features of miR-122 targeting that may offer predictive value for human HCC survival.